Abstract

Compartments and membranes are the basis of cell topology and more than 30% of the human genome codes for membrane proteins. It is possible to represent compartments and membrane proteins in a nominal way with many mathematical formalisms used in systems biology, however few explicitly model the topology of the membranes themselves. Discrete stochastic simulation of molecular kinetics potentially oers the most accurate representation of cell dynamics. Since the details of every molecular interaction in a pathway are often not known, the relationship between chemical species in not necessarily best described by simple mass action chemistry. Moreover, modelling every individual molecular interac- tion in the cell is probably unnecessary and currently impractical. Simulation is a form of computer aided analysis, relying on human inter- pretation to derive meaning. To improve eciency and gain meaning in an automatic way, it is necessary to have a formalism based on a model which has decidable properties. This is a pre-copy-editing, author-produced PDF of an article accepted for publication in Bioinformatics following peer review. The definitive publisher-authenticated version [Sean Sedwards and Tommaso Mazza, Cyto-Sim: a formal language model and stochastic simulator of membrane-enclosed biochemical processes, Bioinformatics, 15 October 2007; 23: 2800 - 2802] is available online at: http://bioinformatics.oxfordjournals.org/ [doi:10.1093/bioinformatics/btm416].